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- PDB-3k05: The crystal structure of MDC1 BRCT T2067D in complex with a minim... -

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Basic information

Entry
Database: PDB / ID: 3k05
TitleThe crystal structure of MDC1 BRCT T2067D in complex with a minimal recognition tetrapeptide with an amidated C-terminus
Components
  • Mediator of DNA damage checkpoint protein 1
  • phospho peptide
KeywordsPROTEIN BINDING / BRCT Domain / protein-peptide complex / phospho protein binding / H2AX / DNA damage response / Cell cycle / DNA damage / DNA repair / Nucleus / Phosphoprotein
Function / homology
Function and homology information


chromatin-protein adaptor activity / DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...chromatin-protein adaptor activity / DNA replication checkpoint signaling / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / positive regulation of transcription initiation by RNA polymerase II / SUMOylation of DNA damage response and repair proteins / histone reader activity / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / site of double-strand break / Processing of DNA double-strand break ends / nuclear body / DNA repair / focal adhesion / DNA damage response / nucleoplasm / nucleus
Similarity search - Function
Regulator of Ty1 transposition protein 107 BRCT domain / BRCT domain / BRCT domain, a BRCA1 C-terminus domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCT domain profile. / BRCT domain ...Regulator of Ty1 transposition protein 107 BRCT domain / BRCT domain / BRCT domain, a BRCA1 C-terminus domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Mediator of DNA damage checkpoint protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.33 Å
AuthorsCampbell, S.J. / Edwards, R.A. / Glover, J.N.
CitationJournal: Structure / Year: 2010
Title: Comparison of the Structures and Peptide Binding Specificities of the BRCT Domains of MDC1 and BRCA1
Authors: Campbell, S.J. / Edwards, R.A. / Glover, J.N.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mediator of DNA damage checkpoint protein 1
B: Mediator of DNA damage checkpoint protein 1
C: phospho peptide
D: phospho peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2888
Polymers44,9204
Non-polymers3684
Water8,431468
1
A: Mediator of DNA damage checkpoint protein 1
C: phospho peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5523
Polymers22,4602
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-8 kcal/mol
Surface area9780 Å2
MethodPISA
2
B: Mediator of DNA damage checkpoint protein 1
D: phospho peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7365
Polymers22,4602
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-8 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.642, 74.580, 103.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer bound to a phospho tetrapeptide. There are 2 biological units in the asymmetric unit (chains A & C and chains B & D

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Components

#1: Protein Mediator of DNA damage checkpoint protein 1 / Nuclear factor with BRCT domains 1


Mass: 21856.256 Da / Num. of mol.: 2 / Fragment: BRCT Domain (UNP residues 1892 to 2089) / Mutation: T2067D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0170, MDC1, NFBD1 / Plasmid: pKM596 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q14676
#2: Protein/peptide phospho peptide


Mass: 603.496 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. The peptide is chemically synthesized.
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: PEG 8000, HEPES, pH 8.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2008
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 97906 / % possible obs: 98.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.33-1.383.70.48995.7
1.38-1.433.90.37997.3
1.43-1.53.90.27397.9
1.5-1.583.90.19998.4
1.58-1.683.90.1598.6
1.68-1.813.90.10999.1
1.81-1.993.80.07699.3
1.99-2.273.70.05799.3
2.27-2.873.70.04699.3
2.87-503.80.03698.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.26 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.49 Å
Translation2.5 Å42.49 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→40.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.444 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20211 4871 5 %RANDOM
Rwork0.18199 ---
obs0.18298 92958 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.082 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.33→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 24 468 3597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223305
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3062.014510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45522.794136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84815.055545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9771530
X-RAY DIFFRACTIONr_chiral_restr0.0780.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222544
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0621.52074
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72723382
X-RAY DIFFRACTIONr_scbond_it2.41331231
X-RAY DIFFRACTIONr_scangle_it3.7284.51123
X-RAY DIFFRACTIONr_rigid_bond_restr1.27733305
X-RAY DIFFRACTIONr_sphericity_free3.8253468
X-RAY DIFFRACTIONr_sphericity_bonded2.83133220
LS refinement shellResolution: 1.329→1.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 336 -
Rwork0.336 6513 -
obs--94.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4983-0.20720.31011.6615-0.51180.87150.0113-0.04130.0145-0.0001-0.0262-0.015-0.00420.02970.01490.0005-0.00250.00060.0206-0.00620.003211.3517-6.3348-18.9133
20.48910.4676-0.02560.9018-0.01710.34290.00950.0259-0.03950.01310.0091-0.02420.00660.0232-0.01870.00440.00770.00250.01790.00050.008618.0702-23.8535-42.3369
31.5115-0.3908-0.2462.5233-0.33593.61-0.01690.0132-0.1668-0.1086-0.01890.01110.1471-0.12690.03580.04710.0010.00290.056-0.00430.05311.0228-11.4171-29.6613
44.95321.3756-1.88159.9675-3.99394.27030.0037-0.095-0.09230.29480.12850.31340.0329-0.0172-0.13220.0272-0.00310.01740.0109-0.0010.024712.9551-19.979-33.3908
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1892 - 2085
2X-RAY DIFFRACTION2B1892 - 2085
3X-RAY DIFFRACTION3C139 - 142
4X-RAY DIFFRACTION4D139 - 142

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